Mitochondrial DNA haplogroup Y is associated to Leigh syndrome in Chinese population

Although Leigh syndrome (LS) is a well characterized clinical mitochondrial disorder; the exact mutation is not found in all cases and it is not clear whether matrilineal background has contributed to this disease. To address this issue, we extensively studied and compared the haplogroup composition of a sample of 171 Chinese LS patients with that of 1597 controls. Our results show that haplogroup Y may increase the risk of LS in Chinese by 2.867 fold (95% CI = 1.135–7.240, P = 0.020). Haplogroup B5 has also this trend (1.737 fold, 95% CI = 0.961–3.139), but with a borderline P-value (P = 0.065). Both haplogroups belong to macro-haplogroup N and share a common reverse mutation on nucleotide position 10398 (A10398G). In fact, the combined haplogroup N with 10398G is also associated with an increased risk for LS (OR = 1.882, 95% CI = 1.134–3.124, P = 0.013).     

Social complexity and linguistic diversity in the Austronesian and Bantu population expansions

Reconstructing the rise and fall of social complexity in human societies through time is fundamental for understanding some of the most important transformations in human history. Phylogenetic methods based on language diversity provide a means to reconstruct pre-historic events and model the transition rates of cultural change through time. We model and compare the evolution of social complexity in Austronesian (n = 88) and Bantu (n = 89) societies, two of the world's largest language families with societies representing a wide spectrum of social complexity. Our results show that in both language families, social complexity tends to build and decline in an incremental fashion, while the Austronesian phylogeny provides evidence for additional severe demographic bottlenecks. We suggest that the greater linguistic diversity of the Austronesian language family than Bantu likely follows the different biogeographic structure of the two regions. Cultural evolution in both the Bantu and Austronesian cases was not a simple linear process, but more of a wave-like process closely tied to the demography of expanding populations and the spatial structure of the colonized regions.     

Mitochondrial DNA diversity and population differentiation in southern East Asia

Mitochondrial DNA (mtDNA) polymorphism has been studied systematically in the Han, Tibeto-Buman, and Hmong-Mien ethnic families of southern East Asia. Only two families in this region, Daic and Austro-Asiatic, were still uninvestigated. Daic is a major ethnic family in South China and Southeast Asia and has a long history. To study mtDNA polymorphism within this family, all the Daic populations of China and some of Vietnam (774 individuals from 30 populations) were typed by HVS-1 region sequencing and by PCR-RFLP assays. The observed high Southern type frequencies (B, F, M7, R) confirmed Daic as a typical Southern group. mtDNAs of other populations (126 individuals from 14 populations) from Austro-Asiatic ethnic families neighboring the Daic were also typed. Networks of mtDNA haplogroups in South China were traced from these new data and those from the literature. Ethnic families share many haplogroups, indicating their common origin. However, the two largest families in South China, Daic, and Hmong-Mien, polarized into several ethnic family specific haplogroups. Haplogroup ages were estimated in the networks of high-frequency haplogroups (B, F, M7, R), and they were found to originate about 50,000 years ago. In contrast, ethnic family specific haplogroups all originated around 20,000 years ago. We therefore conclude that modern humans have lived in South China for a long time, inside-ethnogenesis was a rather late event, and frequent inmixing was taking place throughout. MtDNA data of Daic, Austro-Asiatic and other populations in South China has therefore proven pivotal for studying the human history of East Asia.     

Genetic evidence of range-wide population declines in an Australian marsupial prior to European settlement

Reconstruction of a species demographic history can be used to investigate impacts of environmental change through time. Australia’s mesic biome experienced massive changes during the Holocene, including climate fluctuations, increased human populations, and European settlement. Using microsatellite data from 202 brush-tailed rock-wallabies (Petrogale penicillata) sampled across the species current geographic range, we investigated gene flow and inferred the demographic history of the species to explore the historical impacts of environmental change on this once wide-ranging marsupial mammal. We found high levels of genetic diversity in all colonies, despite very restricted contemporary gene flow and no sign of historical gene flow. Demographic analyses showed that individual populations have low effective population sizes (N _e?<?200). We identified a major historical decline throughout the species range occurring 10,000–1000 years before present, spanning a period with increased El Niño Southern Oscillation activity, increased human population size and establishment of the dingo population. This major decline pre-dates the European settlement of Australia and so places the species most recent dramatic decline into context, suggesting that brushed-tailed rock-wallabies were inherently vulnerable to major changes to their environment.     

Lack of mitochondrial DNA structure in Balkan donkey is consistent with a quick spread of the species after domestication

A total of 132 mtDNA sequences from 10 Balkan donkey populations were analysed to ascertain their regional genetic structure and to contribute to the knowledge of the spreading of the species after domestication. The Balkan donkey sequences were compared with those from 40 Burkina Faso donkeys as an African outgroup to account for possible local Balkan scenarios. The 172 sequences gave 62 different haplotypes (55 in Balkan donkey). Virtually all the analysed populations had haplotypes assigned to either Clade 1 or Clade 2 even though the relative proportion of Clade 1 or 2 haplotypes differed across populations. Geographical maps constructed using factors computed via principal component analysis showed that the Balkan donkey populations are not spatially structured. AMOVA confirmed a lack of genetic structure in Balkan donkey mtDNA. Balkan populations were poorly differentiated (Φ_ST = 0.071). Differentiation between the Balkan donkey and the African outgroup also was low. The lack of correspondence between geographical areas and maternal genetic structure is consistent with the hypothesis suggesting a very quick spread of the species after domestication. The current research illustrates the difficulties to trace routes of expansion in donkey, as the species has no geographical structure.     

Mitochondrial sequence diversity within a subspecies of savanna monkeys (Cercopithecus aethiops) is similar to that between subspecies

Cercopithecus aethiops can be classified into four subspecies by morphology and by geographic distribution. However, the phylogenetic relationship between these subspecies is unclear. We previously found five distinct haplogroups of mitochondrial DNA (mtDNA) in the subspecies C. aethiops aethiops at the restriction fragment length polymorphism (RFLP) level, and found that those haplogroups are parapatrically distributed in their habitat. To determine the relationship between subspeciation and haplogroup formation in a subspecies, we compared mtDNA control region and 12S rRNA gene sequences (approximately 700 bp) in C. a. aethiops, two other subspecies of C. aethiops, and two species of Cercopithecus: The diversity between haplogroups in C. a. aethiops was almost the same as that between subspecies. This similar level of diversification between and within haplogroups may explain why a previously obtained mtDNA tree did not show monophyletic branching according to subspecies.     

The accessory sperm count is related to early embryonic diversity in pigs

In pigs, embryonic diversity has been related to embryonic mortality. The relative importance of differences in the duration of ovulation and in the average accessory sperm count (number of sperm cells in the zona pellucida) between sows as a cause of differences in within-litter embryonic diversity was studied. Two experiments were performed in which sows were either ovulating spontaneously (Experiment 1; n=13) or were induced to ovulate with human chorionic gonadotropin (hCG) (Experiment 2; n=15). The sows were slaughtered at 98+/-8 and 118+/-2 h after ovulation, respectively, for observation of embryonic diversity. The duration of ovulation varied between 1 and 4 h and was on average 1.8+/-0.6 and 2.3+/-0.5 h (P>0.10) for Experiment 1 and 2, respectively. Embryonic development in terms of the number of cell cycles tended to differ between Experiment 1 and 2 (3.5+/-0.8 and 5.6+/-0.5, respectively; P<0.10). Within-litter embryonic diversity (SD of number of cell cycles) was 0.83+/-0.35 and 0.60+/-0.27 (P>0.10), respectively. The average per litter accessory sperm count was variable (ranging from 1 to 75) and was affected by experiment (median: 32+/-27 and 12+/-14, respectively; P<0.05). Within-litter embryonic diversity was not related to the duration of ovulation (P>0.10) but was negatively related to the average or median accessory sperm count (P<0.025). The significant relationship between the accessory sperm count and embryonic diversity suggests that the duration of fertilization is a determinant for embryonic diversity.     

Considerable MHC diversity suggests that the functional extinction of baiji is not related to population genetic collapse

To further extend our understanding of the mechanism causing the current nearly extinct status of the baiji (Lipotes vexillifer), one of the most critically endangered species in the world, genetic diversity at the major histocompatibility complex (MHC) class II DRB locus was investigated in the baiji. Nine highly divergent DRB alleles were identified in 17 samples, with an average of 28.4 (13.2%) nucleotide difference and 16.7 (23.5%) amino acid difference between alleles. The unexpectedly high levels of DRB allelic diversity in the baiji may partly be attributable to its evolutionary adaptations to the freshwater environment which is regarded to have a higher parasite diversity compared to the marine environment. In addition, balancing selection was found to be the main mechanisms in generating sequence diversity at baiji DRB gene. Considerable sequence variation at the adaptive MHC genes despite of significant loss of neutral genetic variation in baiji genome might suggest that intense selection has overpowered random genetic drift as the main evolutionary forces, which further suggested that the critically endangered or nearly extinct status of the baiji is not an outcome of genetic collapse.     

Mitochondrial DNA (COI) analyses reveal that amphipod diversity is associated with environmental heterogeneity in deep‐sea habitats

The relationship between species diversity and environmental parameters is poorly understood for the mobile macrofauna of deep‐sea habitats due to under‐sampling and subsequent lack of accurate taxonomic information. To redress this, cytochrome oxidase c subunit I (COI) DNA sequences were used to estimate species diversity and to compare phoxocephalid amphipod assemblages among 20 stations encompassing a range of environmental conditions. Two regions, east (Chatham Rise) and west (Challenger Plateau) of New Zealand were sampled to depths of 200–1200 m with an epibenthic sled. Using a comparison among identified morphospecies, we found a clear gap in sequence divergences between 6% and 13% and used a 6% threshold to designate molecular operational taxonomic units (MOTUs), as a surrogate to putative species. DNA sequences (n = 297) revealed high total diversity (n = 49 MOTUs), as well as high beta diversity (28 MOTUs found at single location only). Novel phoxocephalid MOTUs were found at most stations, especially on Challenger Plateau and the flanks of Chatham Rise. Analyses of interstation assemblages revealed a major split between regions, indicating minimal overlap in taxon distributions. A cluster of highly similar stations was identified, broadly distributed over the crest of Chatham Rise, in association with elevated food availability, probably resulting from higher surface productivity and relatively shallow depth. Accordingly, multivariate analysis revealed a strong correlation between phoxocephalid assemblages and food supply. This study highlights the value of molecular approaches, in particular COI sequences, for quantifying and comparing diversity in under‐sampled and/or under‐studied taxa.     

Using model selection to choose a size-based condition index that is consistent with operational welfare indicators

Quantitative and qualitative measures of fish health and welfare are essential for management of both wild capture and aquaculture species. These measures include morphometric body condition indices, energetic condition and aquaculture operational welfare indicators (OWIs). Measures vary in ease of measurement (and may require destructive sampling), and it is critical to know how well they correlate with fish health and welfare so appropriate management decisions can be based on them. Lumpfish (Cyclopterus lumpus) is a new farming species that needs nondestructive OWIs to be developed and validated. In this study, we developed a C. lumpus fin damage score. Four different body condition indexes based on individual weight relative to either length–weight relationships or relative to other fish in its local environment were tested (using model selection) as predictors of individual fin damage. Results showed severity of fin damage was predicted by small size relative to the other individuals in the tank or cage. Body condition based on length–weight relationship was not found to predict fin damage, indicating that using established indices from fisheries or from other species would not predict welfare risks from fin damage. Implications are that especially in hatchery conditions grading will improve the condition index, and is expected to mitigate fin damage, but that low weight at length was not of use in predicting fin damage. Model selection to choose between a suite of possible indices proved powerful and should be considered in other applications where an easily measured index is needed to correlate with other health measures.     

Mitochondrial haplotypes of European wild boars with 2n = 36 are closely related to those of European domestic pigs with 2n = 38

Wild boars from Western Europe have a 2n = 36 karyotype, in contrast to a karyotype of 2n = 38 in wild boars from Central Europe and Asia and in all domestic pigs. The phylogenetic status of this wild boar population is unclear, and it is not known if it has contributed to pig domestication. We have now sequenced the mtDNA control region from 30 European wild boars (22 with a confirmed 2n = 36 karyotype) and six Asian wild boars (two Hainan and four Dongbei wild boars) to address this question. The results revealed a close genetic relationship between mtDNA haplotypes from wild boars with 2n = 36 to those from domestic pigs with 2n = 38. Thus, we cannot exclude the possibility that wild boars with 2n = 36 may have contributed to pig domestication despite the karyotype difference. One of the European wild boars carried an Asian mtDNA haplotype, and this most likely reflects gene flow from domestic pigs to European wild boars. However, this gene flow does not appear to be extensive because the frequency of Asian haplotypes detected among European wild boars (c. 3%) were 10-fold lower than among European domestic pigs (c. 30%). Previous studies of mtDNA haplotypes have indicated that pig populations in Europe and Asia have experienced a population expansion, but it is not clear if the expansion occurred before or after domestication. The results of the present study are consistent with an expansion that primarily occurred prior to domestication because the mtDNA haplotypes found in European and Asian wild boars did not form their own clusters but were intermingled with haplotypes found in domestic pigs, indicating that they originated from the same population expansion.     

Mitochondrial haplogroups and polymorphisms reveal no association with sporadic prostate cancer in a southern European population

Background

It is known that mitochondria play an important role in certain cancers (prostate, renal, breast, or colorectal) and coronary disease. These organelles play an essential role in apoptosis and the production of reactive oxygen species; in addition, mtDNA also reveals the history of populations and ancient human migration. All these events and variations in the mitochondrial genome are thought to cause some cancers, including prostate cancer, and also help us to group individuals into common origin groups. The aim of the present study is to analyze the different haplogroups and variations in the sequence in the mitochondrial genome of a southern European population consisting of subjects affected (n = 239) and non-affected (n = 150) by sporadic prostate cancer.

Methodology and Principal Findings

Using primer extension analysis and DNA sequencing, we identified the nine major European haplogroups and CR polymorphisms. The frequencies of the haplogroups did not differ between patients and control cohorts, whereas the CR polymorphism T16356C was significantly higher in patients with PC compared to the controls (p = 0.029). PSA, staging, and Gleason score were associated with none of the nine major European haplogroups. The CR polymorphisms G16129A (p = 0.007) and T16224C (p = 0.022) were significantly associated with Gleason score, whereas T16311C (p = 0.046) was linked with T-stage.

Conclusions and Significance

Our results do not suggest that mtDNA haplogroups could be involved in sporadic prostate cancer etiology and pathogenesis as previous studies performed in middle Europe population. Although some significant associations have been obtained in studying CR polymorphisms, further studies should be performed to validate these results.     

The distribution of BoCAL-a alleles in Brassica oleracea is consistent with a genetic model for curd development and domestication of the cauliflower

The characteristic curd of cauliflower (Brassica oleracea var. botrytis L.) consists of proliferating, arrested inflorescence and floral meristems. However, the origins and events leading to the domestication of this important crop trait remain unclear. A similar phenotype observed in the ap1-1/cal-1 mutant of Arabidopsis thaliana led to speculation that the orthologous genes from B. oleracea may be responsible for this characteristic trait. We have carried out a detailed molecular and genetic study, which allows us to present a genetic model based on segregation of recessive alleles at specific, mapped loci of the candidate genes BoCAL and BoAP1. This accounts for differences in stage of arrest between cauliflower and Calabrese broccoli (B. oleracea var. italica Plenck), and predicts the intermediate stages of arrest similar to those observed in Sicilian Purple types. Association of alleles of BoCAL-a with curding phenotypes of B. oleracea is also demonstrated through a survey of crop accessions. Strong correlations exist between specific alleles of BoCAL-a and discrete inflorescence morphologies. These complementary lines of evidence suggest that the cauliflower curd arose in southern Italy from a heading Calabrese broccoli via an intermediate Sicilian crop type. PCR-based assays for the two key loci contributing to curd development are suitable for adoption in marker-assisted selection.     

Mitochondrial gene diversity in Cepaea– population structure, history and positive selection

Previous studies on the geographical distributions of both shell polymorphisms and mitochondrial haplotypes in Cepaea land snails have suggested varying contributions of natural selection, random genetic drift and population history to the origin and persistence of variation. We combine previous studies of polymorphism within two species of Cepaea , with new molecular data from two mitochondrial genes. The distributions of mitochondrial variants suggest that elements of population history may have been influential in creating patterns of diversity. However, some patterns of amino acid substitution that are found in a protein coding gene are also consistent with the action of diversifying selection. This suggests the possibility that in addition to stochastic processes such as repeated founder events, local extinctions and random genetic drift within a structured population, adaptive molecular change may have affected mitochondrial diversity.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87 , 167–184.     

Aphid biodiversity is positively correlated with human population in European countries

At large spatial scales, high numbers of people tend to be located in regions rich in biodiversity. This pattern has been reported for plants, some invertebrate groups, amphibians, reptiles, birds and mammals, but little is known about whether aphids conform to it. Aphids originated from temperate regions of the boreal hemisphere and are thus exceptionally species-poor in the tropics. Here, we test whether aphid species richness is related to human population variation in European countries. The number of aphid species increases significantly with increasing human population size. This happens also when controlling for country area, latitude and plant species richness, which are not factors significantly affecting the response variable in the multivariate model. Given that the species–area and species–people relationships have a slope shallower than 1, small countries have a higher aphid species density relative to area and to people than large ones. There is no evidence that the species-people correlation for aphids in European countries arises because both variables are related to increasing temperature or precipitation. Potential mechanisms underlying the findings could thus be a sampling artefact or an influence of habitat heterogeneity. There is a need for an increase in research, public awareness and conservation of large-scale aphid biodiversity.     

Mitochondrial minisatellite polymorphisms in fodder and sugar beets reveal genetic bottlenecks associated with domestication

Historically, sugar beets were selected from fodder beets. We used mitochondrial minisatellite loci to analyze cytoplasmic genetic diversity in fodder beet and sugar beet. Among the 8 sugar beet accessions examined we identified 3 multi-locus haplotypes. These 3 haplotypes were a subset of 5 haplotypes identified among the 29 fodder beet accessions examined. All but one haplotype in fodder beet comprised, in turn, a subset of 12 haplotypes identified previously in leaf beets. Such apparent decreases in cytoplasmic genetic diversity must result from genetic bottlenecks associated with domestication and the ensuing breeding processes. We also detected the haplotype associated with the male-sterile Owen cytoplasm of sugar beet in the fodder beet gene pool. Furthermore, the presence of a 39 kDa protein associated with the Owen cytoplasm was confirmed in two fodder beet plants by Western blot analysis. These results lead us to speculate that the Owen cytoplasm may have originated in fodder beet, from which sugar beet was derived.